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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Analysis of Poultry-Associated Salmonella enterica to Identify and Characterize Properties and Markers Associated with Egg-Borne Transmission of Illness

Location: Egg Safety and Quality

Title: Population structure of Salmonella enterica subspecies enterica (subspecies 1)

Authors
item Desai, Prerak -
item Porwollik, Steffen -
item Long, Fred -
item Cheng, Pui -
item Weinstock, George -
item Fields, Patricia -
item Weimer, Bart -
item Guiney, Donald -
item Gal-Mor, Ohad -
item Rabsch, Wolfgang -
item Guard, Jean
item Frye, Jonathan
item Mcclelland, Michael -

Submitted to: American Society for Microbiology Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: July 12, 2013
Publication Date: October 5, 2013
Citation: Desai, P.T., Porwollik, S., Long, F., Cheng, P., Weinstock, G.M., Fields, P., Weimer, B., Guiney, D., Gal-Mor, O., Rabsch, W., Guard, J.Y., Frye, J.G., Mcclelland, M. 2013. Population structure of Salmonella enterica subspecies enterica (subspecies 1). American Society for Microbiology Annual Meeting. p. 25.

Technical Abstract: <p>We sequenced and assembled 354 new Salmonella enterica ssp. enterica genomes. These genomes were chosen to maximize genetic diversity, representing at least 100 different serovars and distinct PFGE patterns within these serovars. 119 of the strains were of known antibiotic resistance, and were selected to encompass over 50 different patterns of resistance. These new sequences were analyzed together with 350 publically available Salmonella genomes. Whole genome alignments were used to identify regions shared by all genomes, and a maximum likelihood taxonomic tree was constructed. Using a threshold of 0.008 substitutions per site, we identified at least ten deep rooting taxonomic groups within S. enterica ssp. enterica. One of the clades (Clade A) contained nine of the twenty most frequently isolated serovars from human sources - Enteritidis, Typhimurium, Newport, Heidelberg, I 4,[5],12:i:-, Saintpaul, Muenchen, Hadar and Thompson. Clade B contained four of the twenty most frequently isolated serovars from human sources - Javiana, Montevideo, Branderup and Schwarzengrund. Strains within each serovar were generally extremely similar. Assuming the commonly accepted divergence rate of 3.5 x 10-9 substitutions per site per year, the strains sampled for most serovars apparently diverged from each other only a few tens of thousands of years ago[MM1] , Age estimates among strains sampled within individual serovars using Bayesian methods calculated based on tip dating ranged from 900 to 35 years. In some cases these will be over-estimates because unrecognized recombination events will tend to make strains appear more divergent than the unrecombined portions of the genome actually are, Large scale genome chimerism which was previously reported between the closely related serovars Typhi and Paratyphi A was observed in almost all of the heavily sampled serovars we have examined to date. The observed pangenome of 590 annotated Salmonella genomes contained ~23,000 highly supported gene families based on OrthoMCL analysis. In conclusion we have created a valuable public resource of taxonomically diverse Salmonella sequences and associated metadata which would be useful for molecular epidemiology as well as to address fundamental questions pertaining to evolution of serovars and individual gene families, antibiotic resistance and patterns of lateral gene transfer.

Last Modified: 10/1/2014
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